- New Tool: tRNAScan-SE November 9, 2020 - Another tRNA prediction tool has been added to the CPT Galaxy repertoire: tRNAScan-SE. In version 2.0, the default is set to use the bacterial model for prediction on any input nucleotide fasta. Accompanying tRNAScan-SE is a format conversion script Convert tRNAscan-SE table to gff format, written in-house by Anthony Criscione, that allows this data toLearn More...
- Tool Spotlight: Charges November 6, 2020 - A clean representation of protein primary sequence can do wonders for making a compelling case about protein fold or function. The Charges tool allows you to annotate custom residue combinations with user-specified colors. The output is a scalable vector graphic file that can be used to make high-quality figures from any protein fasta input. PresetLearn More...
- New Tool: Linear Genome Plot November 4, 2020 - Draw detailed gene maps for your linear phage genome genbank files using Linear Genome Plot. This new tool has flexible options for genome display on a single or multiple lines with coloring feature shapes based on type (gene, regulatory, etc.) or name (such as product). Label source and placement are also set by the user.Learn More...
- Workflow update: Functional flow faster! November 3, 2020 - The BLAST jobs traditionally found in the PAP Functional Workflow have been tweaked. The BLASTp jobs were the reason that a functional flow took overnight to complete. As of PAP Functional Workflow v2020.07, BLASTp will no longer be run against Bacterial sequences in the NCBI nonredundant (nr) database. By removing BLASTp against all Bacteria (taxidLearn More...
- Paper describing CPT Galaxy for phage annotation published November 3, 2020 - The CPT has been building the infrastructure and resources to be the world leaders in phage annotation using the open-source Galaxy and Apollo platforms since 2015. In our latest manuscript, published this week in PLOS Computational Biology, we describe in detail the tools and workflows that are the mainstays for all phage annotation efforts hereLearn More...
- CPT Galaxy Workflow Updates – October 2020 October 27, 2020 - Howdy all! We have now released fully updated and tested workflows for the Structural and Functional workflows on CPT Galaxy, as well as the other Apollo bridge workflows for loading custom tracks. We have also updated our training material site to include the new UI for both Galaxy and Apollo. Please take a look hereLearn More...
- CPT Galaxy 20.05 and Apollo 2.6.1 Update Known Issues August 21, 2020 - Howdy all! As most of you know, we pushed out some major upgrades to our main services, Galaxy and Apollo, this past Monday. It gave us many new features such as propagating dataset nametags, upgraded workflow management, faster UI for both services, additional annotation control in Apollo, and many more (that will be in aLearn More...
- Summer Upgrades and Maintenance Downtime August 12, 2020 - We are going to be down for the majority of next Monday, August 17th 2020, for planned system downtime while we perform required maintenance on the machines, but also on upgrading our Galaxy and Apollo instances!
- Maintenance Scheduled for Thursday June 4 June 3, 2020 - Howdy all! CPT’s services will be down for several hours tomorrow for regular OS maintenance as well as full implementation of some procedures to deal with added load over the last few weeks. We may wrap things up sooner, but the full window is as below. The admin team thanks you for your patience asLearn More...
- New Tool: Remove FASTA Sequences from .gff3 File May 12, 2020 - Ever need to use a program that takes a gff3 format, but can’t have the FASTA sequence at the end? With this tool, that problem is solved! Galaxy now has a simple tool to remove the FASTA sequence from the end of a gff3 file, making it a simple transition to pipe your gff3 intoLearn More...